X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.7
Temperature 277.0
Details 22% PEG8000, 0.2M ammonium sulfate, 0.1M sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.63 α = 90
b = 65.87 β = 90
c = 104.67 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2012-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.7 50 100.0 0.102 -- -- 7.2 -- 22473 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.7 1.76 100.0 0.409 -- 6.1 7.3 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
SAD 1.7 50.0 -- 0.0 -- 22306 1119 99.96 -- 0.1473 0.145 0.1925 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.7 1.744 -- 83 1462 0.163 0.234 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.5542
Anisotropic B[1][1] -0.29
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.64
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.35
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 12.809
r_sphericity_free 28.393
r_rigid_bond_restr 2.101
r_gen_planes_refined 0.006
r_chiral_restr 0.087
r_dihedral_angle_4_deg 9.583
r_dihedral_angle_3_deg 12.595
r_dihedral_angle_2_deg 34.952
r_dihedral_angle_1_deg 5.207
r_angle_refined_deg 1.269
r_bond_refined_d 0.008
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1361
Nucleic Acid Atoms 0
Heterogen Atoms 66
Solvent Atoms 242

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Phenix Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.6.0117 refinement